Variant report

Variant	rs72959240
Chromosome Location	chr1:93731037-93731038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93728185..93731169-chr1:93735951..93738017,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10489733	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11799543	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799928	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800760	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802420	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802421	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11802822	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11805267	1.00[EUR][1000 genomes]
rs11807404	0.91[AMR][1000 genomes]
rs11808445	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11809153	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239183	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28829343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41528947	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55734759	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55738503	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55741554	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56281837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56657492	0.82[ASN][1000 genomes]
rs58505360	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58770710	1.00[EUR][1000 genomes]
rs58807475	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59368083	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59609847	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59774396	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60079850	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60497651	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60813039	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61252284	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61335636	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61671588	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61690932	1.00[EUR][1000 genomes]
rs61729705	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541348	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541360	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6541398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663752	1.00[EUR][1000 genomes]
rs6664190	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6667540	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671070	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6675991	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677114	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679304	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6679630	1.00[ASN][1000 genomes]
rs6688199	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689867	1.00[EUR][1000 genomes]
rs6695142	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701683	1.00[ASN][1000 genomes]
rs6704067	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955402	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72957210	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72957220	0.82[ASN][1000 genomes]
rs72957300	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72959204	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959216	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959225	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72959255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959273	1.00[ASN][1000 genomes]
rs72961310	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72961322	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72961328	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74101458	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74101470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74104014	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104019	1.00[EUR][1000 genomes]
rs7512471	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518171	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7518930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529230	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7533526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540960	1.00[ASN][1000 genomes]
rs7544352	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545154	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545358	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7548629	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754899	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8489	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8561	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324347	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9659202	0.83[AMR][1000 genomes]
rs9662414	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
4	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:93721200-93731400	Weak transcription	NH-A	brain
7	chr1:93724200-93731800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:93725200-93732600	Weak transcription	NHDF-Ad	bronchial
9	chr1:93726400-93731600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:93726400-93731800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr1:93726400-93732000	Weak transcription	Right Ventricle	heart
12	chr1:93726600-93731800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr1:93726600-93731800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr1:93726800-93731200	ZNF genes & repeats	GM12878-XiMat	blood
15	chr1:93726800-93731800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr1:93727000-93731200	ZNF genes & repeats	Dnd41	blood
17	chr1:93727000-93731800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:93727800-93731800	Weak transcription	NHEK	skin
19	chr1:93727800-93741600	Weak transcription	Fetal Kidney	kidney
20	chr1:93728600-93731600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:93728600-93738400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:93728600-93741000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:93728600-93741400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:93728600-93751400	Weak transcription	Adipose Nuclei	Adipose
25	chr1:93728600-93754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:93728600-93764400	Weak transcription	Psoas Muscle	Psoas
27	chr1:93728600-93769400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:93728600-93770400	Weak transcription	HSMM	muscle
29	chr1:93728800-93731200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:93728800-93731200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:93728800-93731200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:93728800-93731600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:93728800-93732200	Weak transcription	HMEC	breast
34	chr1:93728800-93732600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:93728800-93732800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:93728800-93736000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:93728800-93740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:93728800-93740400	Weak transcription	Liver	Liver
39	chr1:93728800-93740400	Weak transcription	Fetal Intestine Large	intestine
40	chr1:93728800-93746600	Weak transcription	Aorta	Aorta
41	chr1:93728800-93751600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:93728800-93751800	Weak transcription	Placenta	Placenta
43	chr1:93728800-93752600	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:93728800-93752600	Weak transcription	Fetal Stomach	stomach
45	chr1:93728800-93753800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:93728800-93754800	Weak transcription	Ovary	ovary
47	chr1:93728800-93755000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:93728800-93755000	Weak transcription	Left Ventricle	heart
49	chr1:93728800-93755000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:93728800-93778200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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